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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatgggtagaacacttggtttatgtttataatgcctgcttgttgaatgatattggttgacttaaacgtaaacttaggaaacgatttctctgttctgcagGGTGTTGATTTTTGGGCCATCAACACAGATGTTCAAGCTTTGCAGAAATCACAAGCCGAACATCGCGTTCAAATCGGCGAAGCTTTGACCCGAGGACTTG

Basic information

species Physcomitrella patens
transcript PP1S275_2V6.1
intron # 1
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|100356004|gb|BY946147.1|BY946147
EST:     GCGGCGGGGGCAACAATGCTGTGAACCGCATGATTGGGAGCGGCATTCAG                         GGTGTTGATTTTTGGGCCATCAACACAGATGTTCAAGCTTTGCAGAAATCA
genomic: GCGGCGGGGGCAACAATGCTGTGAACCGCATGATTGGGAGCGGCATTCAGgtttgttgat ... tgttctgcagGGTGTTGATTTTTGGGCCATCAACACAGATGTTCAAGCTTTGCAGAAATCA
EST: gi|67719210|gb|BJ969469.1|BJ969469
EST:     GCGGCGGGGGCAACAATGCTGTGAACCGCATGATTGGGAGCGGCATTCAG                         GGTGTTGATTTTTGGGCCATCAACACAGATGTTCAAGCTTTGCAGAAATCA
genomic: GCGGCGGGGGCAACAATGCTGTGAACCGCATGATTGGGAGCGGCATTCAGgtttgttgat ... tgttctgcagGGTGTTGATTTTTGGGCCATCAACACAGATGTTCAAGCTTTGCAGAAATCA
EST: gi|100443253|gb|BY963549.1|BY963549
EST:     GCGGCGGGGGCAACAATGCTGTGAACCGCATGATTGGGAGCGGCATTCAG                         GGTGTTGATTTTTGGGCCATCAACACAGATGTTCAAGCTTTGCAGAAATCA
genomic: GCGGCGGGGGCAACAATGCTGTGAACCGCATGATTGGGAGCGGCATTCAGgtttgttgat ... tgttctgcagGGTGTTGATTTTTGGGCCATCAACACAGATGTTCAAGCTTTGCAGAAATCA
EST: gi|100399117|gb|BY954208.1|BY954208
EST:     GCNGCGGGGGCAACAATGCTGTGAACCGCATGATTGGGAGCGGCATTCAG                         GGTGTTGATTTTTGGGC-ATCAACACAGATGTTCAAGCTTTGCAGAAATCA
genomic: GCGGCGGGGGCAACAATGCTGTGAACCGCATGATTGGGAGCGGCATTCAGgtttgttgat ... tgttctgcagGGTGTTGATTTTTGGGCCATCAACACAGATGTTCAAGCTTTGCAGAAATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgatattggttgacttaaacgtaaacttaggaaacgatttctctgttctgcagGGTGTTGATTTTTGGGCCATCAACACAGATGTTCAAGCTTTGCAGAAATCACAAGCCGAACATCGCGTTCAAATCGGCGAAGCTTTGACCCGAGGACTTG
         ggttgac  putative branch site (score: 4)
                                       tttctctgttctgc  putative PPT
                       taaactta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatgggtagaacacttggtttatgtttataatgcctgcttgttgaatgatattggttgacttaaacgtaaacttaggaaacgatttctctgttctgcagGGTGTTGATTTTTGGGCCATCAACACAGATGTTCAAGCTTTGCAGAAATCACAAGCCGAACATCGCGTTCAAATCGGCGAAGCTTTGACCCGAGGACTTG

- - - - - - - - - - - - - - - - - - - - tgttgaa